From 988726f6b719e2ed3603a294c70069ad477ea4e3 Mon Sep 17 00:00:00 2001
From: Justin Kong <64031655+JustKong13@users.noreply.github.com>
Date: Wed, 19 May 2021 23:18:09 -0400
Subject: [PATCH] added entire pathway

---
 added_reactions/cmpacna.py | 106 +++++++++++++++++++++++++++++++++++--
 1 file changed, 101 insertions(+), 5 deletions(-)

diff --git a/added_reactions/cmpacna.py b/added_reactions/cmpacna.py
index fddbdba..0696cb9 100644
--- a/added_reactions/cmpacna.py
+++ b/added_reactions/cmpacna.py
@@ -1,4 +1,100 @@
-# cmpacna reactions
+# cmpacna reactions "cmpacna_c": 0.08657083577
+
+# EC number 5.3.1.19 https://biocyc.org/META/NEW-IMAGE?type=REACTION&object=L-GLN-FRUCT-6-P-AMINOTRANS-RXN
+
+f6p = model.metabolites.get_by_id("f1p_c")
+gln__L = model.metabolites.get_by_id("gln__L_c")
+gam6p = model.metabolites.get_by_id("gam6p_c")
+glu__L= model.metabolites.get_by_id("glu__L_c")
+
+l_gln_fruct_6_p_aminotrans_rxn = Reaction("L-GLN-FRUCT-6-P-AMINOTRANS-RXN")
+l_gln_fruct_6_p_aminotrans_rxn.name = "L-GLN-FRUCT-6-P-AMINOTRANS-RXN"
+l_gln_fruct_6_p_aminotrans_rxn.add_metabolites(
+    {
+        f6p: -1.0,
+        gln__L: -1.0,
+        gam6p: 1.0,
+        glu__L:1.0
+    }
+)
+
+# EC number 5.4.2.10 https://biocyc.org/gene?orgid=META&id=EG11553#tab=RXNS
+
+gam6p = model.metabolites.get_by_id("gam6p_c")
+gam1p = model.metabolites.get_by_id("gam1p_c")
+
+rxn_5_4_2_10 = Reaction("5.4.2.10-RXN")
+rxn_5_4_2_10.name = "rxn_5_4_2_10"
+rxn_5_4_2_10.subsystem = "UDP-N-acetyl-D-glucosamine biosynthesis I",
+rxn_5_4_2_10.add_metabolites(
+    {
+        gam6p:-1.0,
+        gam1p:1.0
+    }
+)
+
+# EC number 2.3.1.157 https://biocyc.org/META/NEW-IMAGE?type=REACTION&object=2.3.1.157-RXN
+
+accoa = model.metabolites.get_by_id("accoa_c")
+gam1p = model.metabolites.get_by_id("gam1p_c")
+acgam1p = model.metabolites.get_by_id("acgam1p_c")
+coa = model.metabolites.get_by_id("coa_c")
+h = model.metabolites.get_by_id("h_c")
+
+rxn_2_3_1_157 = Reaction("2.3.1.157-RXN")
+rxn_2_3_1_157.name = "2.3.1.157-RXN"
+rxn_2_3_1_157.subsystem = "UDP-N-acetyl-D-glucosamine biosynthesis I"
+rxn_2_3_1_157.add_metabolites(
+    {
+        accoa: -1.0,
+        gam1p: -1.0,
+        acgam1p: 1.0,
+        coa: 1.0,
+        h: 1.0
+    }
+)
+
+# EC number 2.7.7.23 https://biocyc.org/META/NEW-IMAGE?type=REACTION&object=NAG1P-URIDYLTRANS-RXN
+
+utp = model.metabolites.get_by_id("utp_c")
+acgam1p = model.metabolites.get_by_id("acgam1p_c")
+h = model.metabolites.get_by_id("h_c")
+uacgam = model.metabolites.get_by_id("uacgam_c")
+ppi = model.metabolites.get_by_id("ppi_c")
+
+nag1p_uridyltrans_rxn = Reaction("NAG1P-URIDYLTRANS-RXN")
+nag1p_uridyltrans_rxn.name = "NAG1P-URIDYLTRANS-RXN"
+nag1p_uridyltrans_rxn.subsystem = "UDP-N-acetyl-D-glucosamine biosynthesis I"
+nag1p_uridyltrans_rxn.add_metabolites(
+    {
+        utp: -1.0,
+        acgam1p: -1.0,
+        h:-1.0,
+        uacgam: 1.0,
+        ppi: 1.0
+    }
+)
+
+# EC number 3.2.1.183 https://biocyc.org/META/NEW-IMAGE?type=REACTION&object=RXN-9987 
+
+uacgam = model.metabolites.get_by_id("uacgam_c")
+h2o = model.metabolites.get_by_id("h2o_c")
+acmana = model.metabolites.get_by_id("acmana_c")
+udp = model.metabolites.get_by_id("udp_c")
+h = model.metabolites.get_by_id("h_c")
+
+rxn_9987 = Reaction("RXN-9987")
+rxn_9987.name = "RXN-9987"
+rxn_9987.subsystem = "CMP-N-acetylneuraminate biosynthesis II"
+rxn_9987.add_metabolites(
+    {
+        uacgam: -1.0,
+        h2o: -1.0,
+        acmana: 1.0,
+        udp: 1.0,
+        h: 1.0
+    }
+)
 
 
 # EC number 2.5.1.56 https://biocyc.org/META/NEW-IMAGE?type=REACTION&object=N-ACETYLNEURAMINATE-SYNTHASE-RXN
@@ -16,6 +112,7 @@
 
 N_acetylneuraminate_synthesis_rxn = Reaction("ACES")
 N_acetylneuraminate_synthesis_rxn.name = "N-ACETYLNEURAMINATE SYNTHASE RXN"
+N_acetylneuraminate_synthesis_rxn.subsystem = "CMP-N-acetylneuraminate biosynthesis II"
 N_acetylneuraminate_synthesis_rxn.add_metabolites(
     {
         pep: -1.0,
@@ -42,6 +139,7 @@
 
 cmpacna_production_rxn = Reaction("CMPACNA_rxn")
 cmpacna_production_rxn.name = "N-acylneuraminate cytidylyltransferase"
+cmpacna_production_rxn.subsystem = "CMP-N-acetylneuraminate biosynthesis II"
 cmpacna_production_rxn.add_metabolites(
     {
         ncma: -1.0,
@@ -54,13 +152,11 @@
 
 
 
-
 model.add_reactions(
     [
-        N_acetylneuraminate_synthesis_rxn, cmpacna_production_rxn
+        cmpacna_production_rxn, N_acetylneuraminate_synthesis_rxn, rxn_9987, nag1p_uridyltrans_rxn, rxn_2_3_1_157, rxn_5_4_2_10, l_gln_fruct_6_p_aminotrans_rxn
     ]
 )
 
-cobra.io.save_json_model(model, "iML1515_cmpacna.json")
-
 model.optimize().objective_value
+cobra.io.save_json_model(model, "./models/iML1515_cmpacna.json")